Frontiers in Computational Chemistry

Volume 1

by

Zaheer Ul-Haq, Jeffry D. Madura

DOI: 10.2174/97816080586481150101
eISBN: 978-1-60805-864-8, 2015
ISBN: 978-1-60805-865-5
ISSN: 2352-944X (Print)
ISSN: 2352-9458 (Online)



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Computational chemistry is a very diverse field spanning from the development and application of linear free energy relationships (QSAR, QSPR), to ...[view complete introduction]

Table of Contents

Foreword

- Pp. i-ii (2)

Zaheer-ul-Haq and J. D. Madura

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List of Contributors

- Pp. iii-v (3)

Zaheer-ul-Haq and J. D. Madura

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Computational Strategies to Incorporate GPCR Complexity in Drug Design

- Pp. 3-43 (41)

Maria Marti-Solano, Agnieszka A. Kaczor, Ramon Guixà-González and Jana Selent

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Knowledge-Based Drug Repurposing: A Rational Approach Towards the Identification of Novel Medical Applications of Known Drugs

- Pp. 44-81 (38)

Carolina L. Bellera, Mauricio E. Di Ianni, María L. Sbaraglini, Eduardo A. Castro, Luis E. Bruno-Blanch and Alan Talevi

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Tuning the Solvation Term in the MM-PBSA/GBSA Binding Affinity Predictions

- Pp. 82-120 (39)

Irene Maffucci and Alessandro Contini

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Recent Advances in the Discovery and Development of Protein- Protein Interaction Modulators by Virtual Screening

- Pp. 121-157 (37)

Dik-Lung Ma, Li-Juan Liu, Sheng Lin, Modi Wang, Daniel Shiu-Hin Chan and Chung-Hang Leung

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Computational Design of Biological Systems: From Systems to Synthetic Biology

- Pp. 158-196 (39)

Milsee Mol and Shailza Singh

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Considering the Medium when Studying Biologically Active Molecules: Motivation, Options and Challenges

- Pp. 197-256 (60)

Liliana Mammino and Mwadham M. Kabanda

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A Novel Coarse-Grained Description of Protein Structure and Folding by UNRES Force Field and Discrete Nonlinear Schrödinger Equation

- Pp. 257-289 (33)

Adam Liwo, Antti Niemi, Xubiao Peng and Adam K. Sieradzan

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Computational Chemistry Strategies Tackling Function and Inhibition of Pharmaceutically Relevant Targets

- Pp. 290-343 (54)

Michele Cascella, Matteo Dal Peraro and Marco De Vivo

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Subject Index

- Pp. 344-350 (7)

Zaheer-ul-Haq and J. D. Madura

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Preface

Computational chemistry is a very diverse field spanning from the development and application of linear free energy relationships (e.g. QSAR, QSPR), to electronic structure calculations, molecular dynamics simulations, and to solving coupled differential equations (e.g. drug metabolism). The focus of Frontiers in Computational Chemistry is to present material on molecular modeling techniques used in drug discovery and the drug development process. Topics falling under this umbrella include computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity. In this volume, we have collected eight different perspectives in the application of computational methods towards drug design. In chapter 1 “Computational Strategies to Incorporate GPCR Complexity in Drug Design” the authors review various computational approaches to G protein-coupled receptors (GPCRs). They review the use of GPCR databases to extract starting information about the structure and function of these systems. The authors also review different strategies currently being probe the molecular mechanisms of drug action as well as the development of new drugs.

The topic of chapter 2 “Knowledge-Based Drug Repurposing: A Rational Approach Towards the Identification of Novel Medical Applications of Known Drugs” is of current interest in the pharmaceutical industry. As we learn more about the biochemical pathways and the interactions of compounds with proteins of these pathways, one can gain an appreciation of how current and previous drugs can be used for other medical uses. This chapter discusses the use of cheminformatics and bioinformatics in identifying new insights about known drugs. Chapter 3, “Tuning the Solvation Term in the MM-PBSA/GBSA Binding Affinity Predictions” focuses on the development and application of a computational tool. A widely used method, Molecular Mechanics Poisson-Boltzmann (Generalized Born) Surface Area (MM-PBSA, MMGBSA), is discussed in terms of applying the method to calculate accurate binding affinities. The authors point out that in order to obtain good, reliable results the MM-PBSA or MM-GBSA methods need to be tuned for a particular system. In particular, they focus on interior dielectric constant as well as the PB and GB solvers.

A very active area of experimental and computational research is protein-protein interactions that is the topic of Chapter 4, “Recent Advances in the Discovery and Development of Protein-Protein Interaction Modulators by Virtual Screening”. In particular, the application of virtual screening methods to find compounds that modulate protein-protein interactions. This is a very challenging task since protein interfaces are flat, large, and lack distinct features. The authors provide a review of the use of virtual screening in protein-protein interactions as its role in drug discovery. Across the scientific field, we come across the term “big data.” In particular, that data generated from genomic projects is overwhelming. In Chapter 5 “Computational Design of Biological Systems: From Systems to Synthetic Biology” the authors describe the development and use of computational methods on large biological data sets to potentially engineer circuits. This systems biology approach to understanding biological function is being used to develop synthetic biological systems. Such developments have potential uses in biotechnology and in the development of strategies to treat various diseases such as cancer.

Biological systems are complex systems to study. In Chapter 6, “Considering the Medium when Studying Biologically Active Molecules: Motivation, Options and Challenges” we are reminded that when studying biological systems not to forget the environment surrounding the system. Most of the time, the environment is left out due to its complexity; however, one must keep in mind that the environment may play a significant role in biological activity. The authors review some insight into how to appropriately include the environment into the study of a particular biological system. As computational power, hardware and software, continue to increase so do the systems, both temporally and spatially. One approach to address the increase in systems is presented in Chapter 7 “New frontiers of coarse-grained approach to protein folding.” Coarse-graining involves the reduction in the number of particles of the system by representing a small group of particles, e.g. an amino side-chain by a single particle. This reduction in the number of particles to represent a biological system has the potential to allow for greater exploration of the free energy landscape as well as simulation increased timescales. The authors review the use of coarse-graining in the study of protein folding.

The last chapter “Computational chemistry strategies-tackling function and inhibition of pharmaceutically relevant targets” reviews the various computational methods used to identify pharmaceutically relevant targets. The authors illustrate the application of various tools from first principles to empirical methods in the discovery and development of new compounds that potentially lead or become the next drug. They appropriately point out that it is through the combination of experiment and computations that lead to significant advancement in molecular medicine.

Zaheer Ul-Haq
Panjwani Center for Molecular Medicine & Drug Research
International Center for Chemical & Biological Sciences
University of Karachi
Pakistan

&

J. D. Madura
Department of Chemistry & Biochemistry
Center for Computational Sciences
Duquesne University, Pittsburgh
USA

List of Contributors

Editor(s):
Zaheer Ul-Haq
Panjwani Center for Molecular Medicine & Drug Research International Center for Chemical & Biological Sciences
University of Karachi
Karachi
Pakistan


Jeffry D. Madura
Department of Chemistry & Biochemistry
Center for Computational Sciences Duquesne University
Pittsburgh
USA




Contributor(s):
Adam K. Sieradzan
Faculty of Chemistry, University of Gdańsk
Wita Stwosza 63, 80-952 Gdańsk
Poland
/
Department of Physics and Astronomy and Science for Life Laboratory
Uppsala University
P.O. Box 803, S-75108
Uppsala
Sweden


Adam Liwo
Faculty of Chemistry
University of Gdańsk
Wita Stwosza 63, 80-952
Gdańsk
Poland


Agnieszka A. Kaczor
Department of Pharmaceutical Chemistry
University of Eastern Finland, School of Pharmacy
Kuopio
Finland
/
Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Faculty of Pharmacy with Division for Medical Analytics
Medical University of Lublin
Lublin
Poland


Alan Talevi
Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences
National University of La Plata
Buenos Aires
Argentina


Alessandro Contini
Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica “Alessandro Marchesini”
Università degli Studi di Milano
Via Venezian, 21 20133
Milano
Italy


Antti Niemi
Department of Physics and Astronomy and Science for Life Laboratory
Uppsala University
P.O. Box 803, S-75108
Uppsala
Sweden
/
Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson
Université de Tours
Parc de Grandmont, F37200
Tours
France
/
Department of Physics
Beijing Institute of Technology
Haidian District, Beijing 100081
People’s Republic of China


Carolina L. Bellera
Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences
National University of La Plata
Buenos Aires
Argentina


Chung-Hang Leung
State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences
University of Macau
Macao
China


Daniel Shiu-Hin Chan
Department of Chemistry
Hong Kong Baptist University
Kowloon Tong
Hong Kong
China


Dik-Lung Ma
Department of Chemistry
Hong Kong Baptist University
Kowloon Tong
Hong Kong
China


Eduardo A. Castro
Institute of Physicochemical Theoretical and Applied Research (INIFTA)
National Council of Scientific and Technical Research (CONICET) CCT La Plata



Irene Maffucci
Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica “Alessandro Marchesini”
Università degli Studi di Milano
Via Venezian, 21 20133
Milano
Italy


Jana Selent
Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences
Universitat Pompeu Fabra
IMIM (Hospital del Mar Medical Research Institute)
Barcelona
Spain


Li-Juan Liu
State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences
University of Macau
Macao
China


Liliana Mammino
Department of Chemistry
University of Venda
South Africa


Luis E. Bruno-Blanch
Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences,
National University of La Plata
Buenos Aires
Argentina


Marco De Vivo
Drug Discovery and Development
Italian Institute of Technology
Genoa
Italy


María L. Sbaraglini
Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences
National University of La Plata
Buenos Aires
Argentina


Maria Marti-Solano
Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences
Universitat Pompeu Fabra
IMIM (Hospital del Mar Medical Research Institute)
Barcelona
Spain


Matteo Dal Peraro
Institute of Bioengineering, School of Life Sciences, ÉcolePolytechniqueFédérale de Lausanne (EPFL)
Lausanne
Switzerland
/
Swiss Institute of Bioinformatics (SIB)
Lausanne
Switzerland


Mauricio E. Di Ianni
Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences
National University of La Plata
Buenos Aires
Argentina


Michele Cascella
Department of Chemistry and Centre for Theoretical and Computational Chemistry (CTCC)
University of Oslo
Oslo
Norway


Modi Wang
Department of Chemistry
Hong Kong Baptist University
Kowloon Tong
Hong Kong
China


Mwadham M. Kabanda
Department of Chemistry
North-West University (Mafikeng Campus)
South Africa


Rafik Karaman
Bioorganic Chemistry Department
Faculty of Pharmacy Al-Quds University
P.O. Box 20002
Jerusalem
Palestine


Ramon Guixà-González
Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences
Universitat Pompeu Fabra
IMIM (Hospital del Mar Medical Research Institute)
Barcelona
Spain


Sheng Lin
Department of Chemistry
Hong Kong Baptist University
Kowloon Tong
Hong Kong
China


Xubiao Peng
Department of Physics and Astronomy and Science for Life Laboratory
Uppsala University
P.O. Box 803, S-75108
Uppsala
Sweden




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